Read mmCIF File
Read a Protein Data Bank (mmCIF) coordinate file.
read.cif(file, maxlines = -1, multi = FALSE,
rm.insert = FALSE, rm.alt = TRUE, verbose = TRUE)file |
a single element character vector containing the name of the mmCIF file to be read, or the four letter PDB identifier for online file access. |
maxlines |
the maximum number of lines to read before giving up with large files. By default if will read up to the end of input on the connection. |
multi |
logical, if TRUE multiple ATOM records are read for all models in multi-model files and their coordinates returned. |
rm.insert |
logical, if TRUE PDB insert records are ignored. |
rm.alt |
logical, if TRUE PDB alternate records are ignored. |
verbose |
print details of the reading process. |
The current version of read.cif reads only ATOM/HETATM records
and creates a pdb object of the data.
See read.pdb for more info.
Returns a list of class "pdb" with the following components:
atom |
a data.frame containing all atomic coordinate ATOM and HETATM data, with a row per ATOM/HETATM and a column per record type. See below for details of the record type naming convention (useful for accessing columns). |
xyz |
a numeric matrix of class |
calpha |
logical vector with length equal to |
call |
the matched call. |
Lars Skjaerven
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## Read a mmCIF file from the RCSB online database
# cif <- read.cif("1hel")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.